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The unusual and dynamic character of PX-DNA.

Niu D, Jiang H, Sha R, Canary JW, Seeman NC - Nucleic Acids Res. (2015)

Bottom Line: Some of the structural features of the molecule have been noted previously, but the structure requires further characterization.In comparison with conventional double stranded DNA and with antiparallel DNA double crossover molecules, it is clear that PX-DNA is a more dynamic structure.Furthermore, the spacing between the nucleotide pairs along the helix axis is shorter, suggesting a mixed B/A structure.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, New York University, New York, NY 10003, USA.

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Related in: MedlinePlus

Labeled DNA structures and their corresponding atomic force microscopy (AFM) images. All the characterized DNA structures are 270 nt pairs in length and the separation between adjacent biotin-streptavidin conjugates is 52 or 53 nt pairs in the DS and DX variants, whereas that of the PX variant is 55 nt pairs. (A) Linear labeled DS-DNA. (B) Linear labeled DX-DNA structure. (C) Zigzag labeled DX-DNA structure. (D) Zigzag labeled PX-DNA structure.
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Figure 2: Labeled DNA structures and their corresponding atomic force microscopy (AFM) images. All the characterized DNA structures are 270 nt pairs in length and the separation between adjacent biotin-streptavidin conjugates is 52 or 53 nt pairs in the DS and DX variants, whereas that of the PX variant is 55 nt pairs. (A) Linear labeled DS-DNA. (B) Linear labeled DX-DNA structure. (C) Zigzag labeled DX-DNA structure. (D) Zigzag labeled PX-DNA structure.

Mentions: The first structure we examined was a DNA duplex, expected to assume the B-conformation. For satisfactory visualization resolution, the length of the duplex is 270 bp, roughly 92 nm (12). One strand is labeled with five biotin-streptavidin conjugates with alternate separations of 52 and 53 nt pairs between any two adjacent labels, so as to have all the labels positioned on the same side of the duplex (Figure 2A). The sample was then examined by AFM, and as shown in Figure 2A, the corresponding linear conformation was observed clearly with a frequency of 91%. Zoomed-out AFM images of relevant species are shown in Supplementary Figure S2 to confirm frequencies of occurrence.


The unusual and dynamic character of PX-DNA.

Niu D, Jiang H, Sha R, Canary JW, Seeman NC - Nucleic Acids Res. (2015)

Labeled DNA structures and their corresponding atomic force microscopy (AFM) images. All the characterized DNA structures are 270 nt pairs in length and the separation between adjacent biotin-streptavidin conjugates is 52 or 53 nt pairs in the DS and DX variants, whereas that of the PX variant is 55 nt pairs. (A) Linear labeled DS-DNA. (B) Linear labeled DX-DNA structure. (C) Zigzag labeled DX-DNA structure. (D) Zigzag labeled PX-DNA structure.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4551946&req=5

Figure 2: Labeled DNA structures and their corresponding atomic force microscopy (AFM) images. All the characterized DNA structures are 270 nt pairs in length and the separation between adjacent biotin-streptavidin conjugates is 52 or 53 nt pairs in the DS and DX variants, whereas that of the PX variant is 55 nt pairs. (A) Linear labeled DS-DNA. (B) Linear labeled DX-DNA structure. (C) Zigzag labeled DX-DNA structure. (D) Zigzag labeled PX-DNA structure.
Mentions: The first structure we examined was a DNA duplex, expected to assume the B-conformation. For satisfactory visualization resolution, the length of the duplex is 270 bp, roughly 92 nm (12). One strand is labeled with five biotin-streptavidin conjugates with alternate separations of 52 and 53 nt pairs between any two adjacent labels, so as to have all the labels positioned on the same side of the duplex (Figure 2A). The sample was then examined by AFM, and as shown in Figure 2A, the corresponding linear conformation was observed clearly with a frequency of 91%. Zoomed-out AFM images of relevant species are shown in Supplementary Figure S2 to confirm frequencies of occurrence.

Bottom Line: Some of the structural features of the molecule have been noted previously, but the structure requires further characterization.In comparison with conventional double stranded DNA and with antiparallel DNA double crossover molecules, it is clear that PX-DNA is a more dynamic structure.Furthermore, the spacing between the nucleotide pairs along the helix axis is shorter, suggesting a mixed B/A structure.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, New York University, New York, NY 10003, USA.

Show MeSH
Related in: MedlinePlus